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Old 07-26-2012, 11:48 PM   #1
Junior Member
Location: China

Join Date: Apr 2012
Posts: 8
Default convert bam file to bedgraph format with inconsistent results

Hi, all

I was trying to convert a sam/bam file into bedgraph files using two different approaches, and found that the results are different:

way 1: I used the program 'wiggles' shipped with tophat 1.3.2:

 samtools view part1.bam > part1.sam
 wiggles part1.sam part1.wiggles.bedgraph
way 2: I used the genomeCoverageBed from bedtools v2.16.2:
        samtools sort part1.bam part1.sorted
        genomeCoverageBed -bga -ibam part1.sorted.bam -g  chrom.sizes > part1.bedtool.bedgraph
In the result files, part1.wiggles.bedgraph and part1.bedtool.bedgraph were different in many genomic regions.

Have anyone experienced with this? it's really confusing.

one of the differences was like this:
1 3927 3931 6 | 1 3927 3930 6
1 3931 3935 5 | 1 3930 3931 2
1 3935 4092 4 | 1 3931 3935 1
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